Okay, I believe that I figured it out. I finally took a look at the Sony BDP-S300 manual. It won't output TrueHD or DTS-HD in bitstream form. It will decode them internally, though. If you set the HDMI audio output on the Sony to "Auto", then you'll get Dolby Digital. If you set HDMI audio output to "PCM", then you'll get 5.1 channel linear PCM from it's internal decoder.
So, with that blu-ray player, you won't ever see TrueHD or DTS-HD on your Yamaha display.